                      :-) GROMACS - gmx mdrun, 2020.4 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf      Artem Zhmurov   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2020.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/romi/My Passport/January 19th - Pathogens & allergies/5k59/313k
Process ID:   104381
Command line:
  gmx mdrun -deffnm md_1_20 -cpi md_0_10.cpt -noappend -v

GROMACS version:    2020.4
Verified release checksum is 79c2857291b034542c26e90512b92fd4b184a1c9d6fa59c55f2e24ccf14e7281
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        CUDA
SIMD instructions:  AVX2_256
FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 9.4.0
C compiler flags:   -mavx2 -mfma -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 9.4.0
C++ compiler flags: -mavx2 -mfma -fexcess-precision=fast -funroll-all-loops SHELL:-fopenmp -O3 -DNDEBUG
CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Thu_Feb_10_18:23:41_PST_2022;Cuda compilation tools, release 11.6, V11.6.112;Build cuda_11.6.r11.6/compiler.30978841_0
CUDA compiler flags:-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-Wno-deprecated-gpu-targets;-gencode;arch=compute_35,code=compute_35;-gencode;arch=compute_50,code=compute_50;-gencode;arch=compute_52,code=compute_52;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-gencode;arch=compute_70,code=compute_70;-gencode;arch=compute_75,code=compute_75;-gencode;arch=compute_80,code=compute_80;-use_fast_math;-D_FORCE_INLINES;-mavx2 -mfma -fexcess-precision=fast -funroll-all-loops SHELL:-fopenmp -O3 -DNDEBUG
CUDA driver:        11.60
CUDA runtime:       11.60


Running on 1 node with total 20 cores, 20 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  12th Gen Intel(R) Core(TM) i7-12700K
    Family: 6   Model: 151   Stepping: 2
    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  Hardware topology: Only logical processor count
  GPU info:
    Number of GPUs detected: 1
    #0: NVIDIA NVIDIA GeForce RTX 3070 Ti, compute cap.: 8.6, ECC:  no, stat: compatible


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------


++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
https://doi.org/10.5281/zenodo.4054979
-------- -------- --- Thank You --- -------- --------

Input Parameters:
   integrator                     = md
   tinit                          = 0
   dt                             = 0.002
   nsteps                         = 50050000
   init-step                      = 0
   simulation-part                = 1
   comm-mode                      = Linear
   nstcomm                        = 100
   bd-fric                        = 0
   ld-seed                        = 1032608471
   emtol                          = 10
   emstep                         = 0.01
   niter                          = 20
   fcstep                         = 0
   nstcgsteep                     = 1000
   nbfgscorr                      = 10
   rtpi                           = 0.05
   nstxout                        = 0
   nstvout                        = 0
   nstfout                        = 0
   nstlog                         = 5000
   nstcalcenergy                  = 100
   nstenergy                      = 5000
   nstxout-compressed             = 5000
   compressed-x-precision         = 1000
   cutoff-scheme                  = Verlet
   nstlist                        = 10
   pbc                            = xyz
   periodic-molecules             = false
   verlet-buffer-tolerance        = 0.005
   rlist                          = 1
   coulombtype                    = PME
   coulomb-modifier               = Potential-shift
   rcoulomb-switch                = 0
   rcoulomb                       = 1
   epsilon-r                      = 1
   epsilon-rf                     = inf
   vdw-type                       = Cut-off
   vdw-modifier                   = Potential-shift
   rvdw-switch                    = 0
   rvdw                           = 1
   DispCorr                       = EnerPres
   table-extension                = 1
   fourierspacing                 = 0.16
   fourier-nx                     = 112
   fourier-ny                     = 112
   fourier-nz                     = 112
   pme-order                      = 4
   ewald-rtol                     = 1e-05
   ewald-rtol-lj                  = 0.001
   lj-pme-comb-rule               = Geometric
   ewald-geometry                 = 0
   epsilon-surface                = 0
   tcoupl                         = V-rescale
   nsttcouple                     = 10
   nh-chain-length                = 0
   print-nose-hoover-chain-variables = false
   pcoupl                         = Parrinello-Rahman
   pcoupltype                     = Isotropic
   nstpcouple                     = 10
   tau-p                          = 2
   compressibility (3x3):
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   ref-p (3x3):
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   refcoord-scaling               = No
   posres-com (3):
      posres-com[0]= 0.00000e+00
      posres-com[1]= 0.00000e+00
      posres-com[2]= 0.00000e+00
   posres-comB (3):
      posres-comB[0]= 0.00000e+00
      posres-comB[1]= 0.00000e+00
      posres-comB[2]= 0.00000e+00
   QMMM                           = false
   QMconstraints                  = 0
   QMMMscheme                     = 0
   MMChargeScaleFactor            = 1
qm-opts:
   ngQM                           = 0
   constraint-algorithm           = Lincs
   continuation                   = true
   Shake-SOR                      = false
   shake-tol                      = 0.0001
   lincs-order                    = 4
   lincs-iter                     = 1
   lincs-warnangle                = 30
   nwall                          = 0
   wall-type                      = 9-3
   wall-r-linpot                  = -1
   wall-atomtype[0]               = -1
   wall-atomtype[1]               = -1
   wall-density[0]                = 0
   wall-density[1]                = 0
   wall-ewald-zfac                = 3
   pull                           = false
   awh                            = false
   rotation                       = false
   interactiveMD                  = false
   disre                          = No
   disre-weighting                = Conservative
   disre-mixed                    = false
   dr-fc                          = 1000
   dr-tau                         = 0
   nstdisreout                    = 100
   orire-fc                       = 0
   orire-tau                      = 0
   nstorireout                    = 100
   free-energy                    = no
   cos-acceleration               = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   simulated-tempering            = false
   swapcoords                     = no
   userint1                       = 0
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
   applied-forces:
     electric-field:
       x:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       y:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       z:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
grpopts:
   nrdf:     28753.9      691098
   ref-t:         313         313
   tau-t:         0.1         0.1
annealing:          No          No
annealing-npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0


Reading checkpoint file md_0_10.cpt
  file generated by:     /usr/bin/gmx
  file generated at:     Sun Oct  9 09:41:58 2022

  GROMACS double prec.:  0
  simulation part #:     1
  step:                  50000000
  time:                  100000.000000

  Version mismatch,
    current program: 2020.4
    checkpoint file: 2019.6

The current GROMACS major version is not identical to the one that
generated the checkpoint file. In principle GROMACS does not support
continuation from checkpoints between different versions, so we advise
against this. If you still want to try your luck we recommend that you use
the -noappend flag to keep your output files from the two versions separate.
This might also work around errors where the output fields in the energy
file have changed between the different versions.

Changing nstlist from 10 to 100, rlist from 1 to 1.166

1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread

Non-default thread affinity set, disabling internal thread affinity

Using 20 OpenMP threads 

System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald tables, spacing: 9.33e-04 size: 1073

Generated table with 1083 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1083 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1083 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Using GPU 8x8 nonbonded short-range kernels

Using a dual 8x8 pair-list setup updated with dynamic, rolling pruning:
  outer list: updated every 100 steps, buffer 0.166 nm, rlist 1.166 nm
  inner list: updated every  10 steps, buffer 0.001 nm, rlist 1.001 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  outer list: updated every 100 steps, buffer 0.320 nm, rlist 1.320 nm
  inner list: updated every  10 steps, buffer 0.043 nm, rlist 1.043 nm

Using Lorentz-Berthelot Lennard-Jones combination rule

Long Range LJ corr.: <C6> 3.0525e-04


Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 5644

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 357013 Atoms
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

Started mdrun on rank 0 Sun Mar 24 03:05:56 2024

           Step           Time
       50000000   100000.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    9.60455e+03    2.59307e+04    1.76954e+04    1.56052e+03   -4.25073e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    8.09432e+03    1.51098e+05    7.93898e+05   -4.43965e+04   -5.76737e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    3.19134e+04   -4.77622e+06    9.40680e+05   -3.83554e+06    7.27415e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.14336e+02   -2.01326e+02   -3.74068e+01    4.58125e-06



Received the INT signal, stopping within 100 steps

           Step           Time
       50000800   100001.60000

Writing checkpoint, step 50000800 at Sun Mar 24 03:06:00 2024


   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    9.56511e+03    2.60310e+04    1.74572e+04    1.66633e+03   -4.12033e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    7.99398e+03    1.51397e+05    7.99026e+05   -4.43257e+04   -5.76820e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    3.23295e+04   -4.77118e+06    9.35188e+05   -3.83599e+06    7.27425e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12501e+02   -2.00684e+02    4.91822e+01    4.51851e-06


	<======  ###############  ==>
	<====  A V E R A G E S  ====>
	<==  ###############  ======>

	Statistics over 801 steps using 9 frames

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    9.46580e+03    2.62601e+04    1.75547e+04    1.58985e+03   -4.19521e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    8.09855e+03    1.50760e+05    7.97168e+05   -4.43987e+04   -5.76897e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    3.23205e+04   -4.77435e+06    9.37158e+05   -3.83719e+06    7.27418e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.13159e+02   -2.01346e+02    2.56850e+01    0.00000e+00

          Box-X          Box-Y          Box-Z
    1.73078e+01    1.73078e+01    1.22385e+01

   Total Virial (kJ/mol)
    3.10497e+05    1.87710e+03   -1.20649e+03
    1.96913e+03    3.08499e+05    3.34976e+02
   -1.09038e+03    4.61617e+02    3.09665e+05

   Pressure (bar)
    1.07501e+01   -1.63122e+01    8.28349e+00
   -1.71464e+01    3.63963e+01   -2.44418e+00
    7.23070e+00   -3.59182e+00    2.99086e+01

      T-Protein  T-non-Protein
    3.14139e+02    3.13118e+02


	M E G A - F L O P S   A C C O U N T I N G

 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
 V&F=Potential and force  V=Potential only  F=Force only

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 Pair Search distance check             302.197280        2719.776     0.0
 NxN Ewald Elec. + LJ [F]            271388.392704    17911633.918    97.9
 NxN Ewald Elec. + LJ [V&F]            3083.366528      329920.218     1.8
 1,4 nonbonded interactions              24.230250        2180.722     0.0
 Shift-X                                  3.213117          19.279     0.0
 Bonds                                    4.775562         281.758     0.0
 Propers                                 20.603322        4718.161     0.0
 Impropers                                1.555542         323.553     0.0
 Virial                                  28.921698         520.591     0.0
 Stop-CM                                  3.213117          32.131     0.0
 Calc-Ekin                               57.836106        1561.575     0.0
 Lincs                                    4.520844         271.251     0.0
 Lincs-Mat                               22.607424          90.430     0.0
 Constraint-V                           285.819228        2286.554     0.0
 Constraint-Vir                          28.445904         682.702     0.0
 Settle                                  92.259180       29799.715     0.2
 CMAP                                     0.591939        1006.296     0.0
 Urey-Bradley                            16.752114        3065.637     0.0
-----------------------------------------------------------------------------
 Total                                                18291114.266   100.0
-----------------------------------------------------------------------------


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 1 MPI rank, each using 20 OpenMP threads

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Neighbor search        1   20          9       0.109          7.882   2.6
 Launch GPU ops.        1   20        801       0.081          5.837   1.9
 Force                  1   20        801       0.199         14.377   4.7
 Wait PME GPU gather    1   20        801       0.408         29.423   9.6
 Reduce GPU PME F       1   20        801       0.120          8.636   2.8
 Wait GPU NB local                              0.417         30.107   9.8
 NB X/F buffer ops.     1   20       1593       0.646         46.643  15.2
 Write traj.            1   20          2       0.730         52.702  17.2
 Update                 1   20        801       0.249         18.001   5.9
 Constraints            1   20        801       0.203         14.688   4.8
 Rest                                           1.085         78.293  25.5
-----------------------------------------------------------------------------
 Total                                          4.247        306.589 100.0
-----------------------------------------------------------------------------

               Core t (s)   Wall t (s)        (%)
       Time:       84.936        4.247     2000.0
                 (ns/day)    (hour/ns)
Performance:       32.592        0.736
Finished mdrun on rank 0 Sun Mar 24 03:06:01 2024

